Hye Min Kim

Arcobacter marinus sp. nov.

A slightly curved, rod-shaped marine bacterium, designated strain CL-S1(T), was isolated from near Dokdo, an island in the East Sea, Korea. Cells were Gram-negative and grew well under either aerobic or microaerobic conditions. Analyses of the 16S rRNA and gyrA gene sequences of strain CL-S1(T) revealed an affiliation with the genus Arcobacter within the class Epsilonproteobacteria. Phylogenetic analyses based on 16S rRNA and gyrA gene sequences showed that strain CL-S1(T) formed a robust clade with Arcobacter halophilus LA31B(T), with sequence similarities of 96.1 and 88.2 %, respectively. DNA-DNA relatedness between strain CL-S1(T) and A. halophilus DSM 18005(T) was 44 %, indicating that they represent genomically distinct species. Strain CL-S1(T) grew optimally at 30-37 degrees C, at pH 7 and in the presence of 3-5 % NaCl. The dominant cellular fatty acids were iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (28.4 %), C(16 : 0) (26.2 %) and C(18 : 1)omega7c (22.3 %). The DNA G+C content of strain CL-S1(T) was 28 mol%. Strain CL-S1(T) differed phenotypically from A. halophilus LA31B(T) based on its ability to grow aerobically at 10 degrees C and inability to grow under anaerobic conditions. Based on the data presented, strain CL-S1(T) is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter marinus sp. nov. is proposed. The type strain is CL-S1(T) (=KCCM 90072(T) =JCM 15502(T)).

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0–10 cm to 10–20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen ( and ). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska.

Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton

A rod-shaped marine bacterium, designated CL-Z59(T), was isolated from seawater enriched with zooplankton. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CL-Z59(T) belongs to the genus Nocardioides, the highest level of sequence similarity (99.2%) being found with respect to Nocardioides marinisabuli KCCM 42681(T). However, DNA-DNA hybridization experiments between strain CL-Z59(T) and N. marinisabuli KCCM 42681(T) revealed a mean relatedness value of 33%. Cells were Gram-positive, strictly aerobic and non-motile. Strain CL-Z59(T) grew optimally at pH 6-7 and 25-30 degrees C and at a NaCl concentration of 3%. The isolate was characterized chemotaxonomically as having LL-diaminopimelic acid in the cell wall. The major isoprenoid quinone was MK-8(H(4)) and the predominant cellular fatty acid was iso-C(16:0). The DNA G+C content was 73.3 mol%. On the basis of phylogenetic, genotypic and phenotypic data, strain CL-Z59(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides salarius sp. nov. is proposed. The type strain is CL-Z59(T) (=KCCM 42320(T)=DSM 18239(T)).

DNA barcoding of Orchidaceae in Korea

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF‐atpH IGS, psbK‐psbI IGS and trnH‐psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK‐psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF‐atpH IGS (0.0648), trnH‐psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH‐psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF‐atpH IGS, psbK‐psbI IGS and trnH‐psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

Salinisphaera dokdonensis sp. nov., isolated from surface seawater.

A Gram-negative, strictly aerobic bacterium, designated CL-ES53(T), was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53(T) were short rods and motile by means of monopolar flagella. Strain CL-ES53(T) grew with 4-21 % NaCl (optimum 10 %) and at 5-40 degrees C (optimum 25 degrees C) and pH 5.2-8.8 (optimum pH 6.3-7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C(18 : 1)omega7c (42.0 %), C(18 : 1)omega9c (14.8 %) and C(14 : 0) (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53(T) revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A(T) (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70(T) (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53(T) formed a robust cluster with S. shabanensis E1L3A(T). Although the 16S rRNA gene sequence similarity between strain CL-ES53(T) and S. shabanensis E1L3A(T) was rather high (96.9 %), DNA-DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53(T) was differentiated from S. shabanensis E1L3A(T) and S. hydrothermalis EPR70(T) on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53(T) should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53(T) (=KCCM 90064(T) =DSM 19549(T)).

Characterization of taurine as anti-obesity agent in C. elegans

BackgroundTaurine plays an important role in reducing physiological stress. Recent studies indicated that taurine may serve as an anti-obesity agent at the cellular level. This study characterizes taurine’s potential anti-obesity function in C. elegans, which have become a popular in vivo model for understanding the regulatory basis of lipid biosynthesis and deposition.MethodsTwo strains of C. elegans were raised on a normal or high-fat diet: N2 (normal) and RB1600, a mutant in tub-1 that serves as a tubby homologue and functions parallel to the 3-ketoacyl-CoA thiolase gene (kat-1) in regulating lipid accumulation. Taurine’s effect on lipid deposition was characterized according to assays of Sudan black B staining, triglyceride content measurement, food consumption, and mobility comparison.ResultsWhen N2 was treated with taurine after the culture in the high-fat media, the worms showed lower lipid accumulation in the assays of the Sudan black B staining and the triglyceride quantification. The anti-obesity effect was less evident in the experiment for RB1600. When the amount of taurine was increased for the high-fat-diet-treated N2 strain, fat deposition decreased and mobility increased in a dose-dependent manner. In the food consumption assays, taurine did not cause a significant change in food intake.ConclusionsTaken together, these results strongly imply that taurine plays an important role in reducing fat deposition by modulating cellular pathways for lipid accumulation and stimulating mobility, but not the pathways for lipid biosynthesis and food intake.

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

Taurine reduces ER stress in C. elegans

BackgroundER stress is a strong indicator of whether or not a cell is undergoing physiological stress. C. elegans is a practical system of characterizing the effect of ER stress at the in vivo or organismal level.MethodsThis study characterized taurine’s anti-ER stress potential employing western blotting on ER stress markers and assays of motility, lifespan comparison, and fecundity measurement.ResultsWhen treated with tunicamycin, C. elegans showed the typical ER stress symptoms. It showed a higher expression of hsp-70 and skn-1 than the non-treated control. Survivorship significantly decreased under tunicamycin treatment, and the offspring number also decreased. During the synchronized culture under ER stress conditions, the C. elegans showed early signs of aging especially between L3 and L4 within their life span, along with lowered motility. The worms, however, showed a positive response to the taurine treatment under ER stress conditions.ConclusionsWhen C. elegans were treated with taurine before or after the tunicamycin treatment, they showed a less severe level of ER stress, including an enhanced survivorship, increased motility, and augmented fecundity. Taken together, these results strongly indicate that taurine works positively to cope with ER stress from the organismal perspective.

Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus.

A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.

Combined Effects of Multiple Endoplasmic Reticulum Stresses on Cytokine Secretion in Macrophage

Cells show various stress signs when they are challenged with severe physiological problems. Majority of such cellular stresses are conveyed to endoplasmic reticulum (ER) and unfolded protein response (UPR) serves as typical defense mechanism against ER stress. This study investigated an interaction between ER stress agents using macropage cell line Raw 264.7. When activated by lipopolysaccharide (LPS), the cell lines showed typical indicators of ER stress. Along with molecular chaperones, the activation process leads to the production of additional infl ammatory mediators. Following activation, the macrophage cell line was further treated with TUN and characterized in terms of chaperone expression and cytokine secretion. When treated with TUN, the activated macrophage cell leads to increased secretion of IL-6 although expression of ER stress markers, GRP94 and GRP78 increased. The secretion of cytokines continued until the addition of BFA which inhibits protein targeting from ER to Golgi. However, secretion of cytokines was ceased upon dual treatments with BFA and TG. This result strongly implies that cells may differently deal with various polypeptides depending on the urgency in cellular function under ER stress. Considering IL-6 is one of the most important signal molecules in macrophage, the molecule might be able to circumvent ER stress and UPR to reach its targeting site.